Hi,
it would be great if you can share some of your code, possibly with dummy data.
Instead of interactive zooming with linked x-axes, consider using the new Slider (Range) control or, in R2020b, two coupled sliders for the minimum and maximum x-value to let the user control the range of x-values. This might perform better than linked axes.
Additionally if the data is modified, it is helpful to not regenerate the plot, but just replace the x- or y-values as needed.
I hope that helps. If not, please consider giving us an example so that we can see the issue.
Best wishes,
Harald
P.S.: I notice that you are using release R2020b. Some aspects of performance have improved in newer releases. We would need to find out if this also improves performance in your particular case.